Dear BBers,
I am trying to refine a structure using COOT and Refmac5 and I have some
concerns about overrefinement and x-ray term weight in Refmac5, based on
the fact that during refinement to let R factor to drift too far from Rfree
is not good...
So... First question about that : what is too fa
You dont give the data resolution - that is very important..
I hate this rule bound approach to Rfree - R differences.. but as a guide
No non-crystallographic symmetry.
1A data - you would expect them to be almost equal
3A data - I would expect a difference of at least 10% - once had the
pleasure
Dear Eleanor, dear Michel (?),
A while ago we statistically analysed the distribution of R, Rfree and of their
difference as a function of the logarithm of resolution (Urzhumtsev et al.,
2009, Acta Cryst, D65, 1283-1291).
In this log-scale, the mode values for all three are nearly linear funct
Well, as no one else has come back to you, I wouldn't say 10 % difference between R and R-free is 'bad' and it's certainly not super-bad! It's a bit high, but if you look at the papers by Ian Tickle from the late 90's and others I think you can be reasonably happy with it. I've been told that A N o
Thank you Kay,
Very good points, as always. I was thinking there must be a better
apodization filter than cutoffs and B factors. I'll have to try a
CC1/2-based roll-off. But, I wonder if this could be done better on a
per-reflection basis? Taking advantage of the sigmas? I have tried
usi
I would like to add a small caveat to Eleanor’s rule about a 3% difference
being too low for a structure refined against 3Å data.
If the 3Å data is for a structure that has already been solved at much higher
resolution (e.g. 2Å) and the only difference for the 3Å dataset is a different
ligand (
Randy Read's paper in latest Acta D:
Measuring and using information gained by observing diffraction data
http://journals.iucr.org/d/issues/2020/03/00/ba5308/index.html
seems very relevant to this discussion!
Pavel
On Fri, Mar 6, 2020 at 8:44 AM James Holton wrote:
> Thank you Kay,
>
> Very
In addition to Sacha’s work there are a few older papers by Ian Tickle & Cie.
(summarized in BMC) and a figure of the empirical distributions
http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-24.htm
which are broad and – as mentioned - the actual delta values
Thank you, Bernhard, for poining out this nice paper by Ian, one more that I
missed previously.
Best regards,
Sacha Urzhumtsev
- Le 6 Mar 20, à 19:15, Bernhard Rupp a écrit :
> In addition to Sacha’s work there are a few older papers by Ian Tickle & Cie.
> (summarized in BMC) and a fi
Hi all,
I am trying to run Blend program from CCP4interface (7.0.078) to merge
multiple datasets (9). I am running the CCP4 on Mac mojave 10.14.6 OS and
installed R program in /usr/local/bin/R. In the CCP4 interface, the same
path is added under system administration/configure interface/extern
Dear Ravi Kumar
If I remember correctly, Blend requires the path to the executable Rscript
rather than R. I can't check this now but I can look into it on Monday if
you are still having trouble.
Best wishes
David
On Fri, 6 Mar 2020, 21:02 Reddiravikumar Kumar,
wrote:
> Hi all,
>
> I am try
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